MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b0871 b2925 b2097 b2926 b3617 b0030 b2407 b2883 b2690 b3945 b4381 b2868 b4064 b4464 b0114 b0755 b3612 b0529 b2492 b0904 b1380 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.491266 (mmol/gDw/h)
  Minimum Production Rate : 0.523979 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.251791
  EX_o2_e : 276.241271
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.991446
  EX_pi_e : 2.045814
  EX_so4_e : 0.123710
  EX_k_e : 0.095892
  EX_mg2_e : 0.004262
  EX_ca2_e : 0.002557
  EX_cl_e : 0.002557
  EX_cu2_e : 0.000348
  EX_mn2_e : 0.000339
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992110
  EX_h2o_e : 548.310928
  EX_co2_e : 26.285841
  EX_acald_e : 1.738805
  EX_pyr_e : 1.588513
  Auxiliary production reaction : 0.523979
  EX_ade_e : 0.013185
  DM_mththf_c : 0.000220
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 21-Sep-2023
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